The first time you run a synchronization FTPSync transfers all the files. All subsequent synchronizations only transfer changed files.

This is because FTPSync does not rely on comparing the file timestamps on source vs. destination, as this is sometimes tricky, but instead relies on changes detected between transfers - for this reason the first transfer is full, as there is no record on previous source state.

The ideal scenario for FTPSync is the following:

delete everything from destination

run FTPSync transfer for the first time - it will transfer all the files

use FTPSync for all further synchronization and avoid changing anything on destination via other tools